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Borowska-Zuchowska N, Mykhailyk S, Robaszkiewicz E, Matysiak N, Mielanczyk L, Wojnicz R, Kovarik A, Hasterok R. Switch them off or not: selective rRNA gene repression in grasses. TRENDS IN PLANT SCIENCE 2023; 28:661-672. [PMID: 36764871 DOI: 10.1016/j.tplants.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/11/2023] [Indexed: 05/13/2023]
Abstract
Nucleolar dominance (ND) is selective epigenetic silencing of 35-48S rDNA loci. In allopolyploids, it is frequently manifested at the cytogenetic level by the inactivation of nucleolar organiser region(s) (NORs) inherited from one or several evolutionary ancestors. Grasses are ecologically and economically one of the most important land plant groups, which have frequently evolved through hybridisation and polyploidisation events. Here we review common and unique features of ND phenomena in this monocot family from cytogenetic, molecular, and genomic perspectives. We highlight recent advances achieved by using an allotetraploid model grass, Brachypodium hybridum, where ND commonly occurs at a population level, and we cover modern genomic approaches that decipher structural features of core arrays of NORs.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
| | - Serhii Mykhailyk
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland
| | - Natalia Matysiak
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland
| | - Lukasz Mielanczyk
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland; Silesian Nanomicroscopy Centre in Zabrze, Silesia LabMed - Research and Implementation Centre, Medical University of Silesia, Katowice, Poland
| | - Romuald Wojnicz
- Department of Histology and Cell Pathology, the Medical University of Silesia in Katowice, School of Medicine with the Division of Dentistry, Zabrze, Poland; Silesian Nanomicroscopy Centre in Zabrze, Silesia LabMed - Research and Implementation Centre, Medical University of Silesia, Katowice, Poland
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, CZ-61200 Brno, Czech Republic
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice 40-032, Poland.
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Cytomolecular Organisation of the Nuclear Genome. Int J Mol Sci 2022; 23:ijms232113028. [PMID: 36361813 PMCID: PMC9656038 DOI: 10.3390/ijms232113028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 11/28/2022] Open
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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Rosselló JA, Maravilla AJ, Rosato M. The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:788911. [PMID: 35283933 PMCID: PMC8908318 DOI: 10.3389/fpls.2022.788911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/27/2022] [Indexed: 05/04/2023]
Abstract
The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.
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Borowska-Zuchowska N, Robaszkiewicz E, Mykhailyk S, Wartini J, Pinski A, Kovarik A, Hasterok R. To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum. FRONTIERS IN PLANT SCIENCE 2021; 12:768347. [PMID: 34938308 PMCID: PMC8685274 DOI: 10.3389/fpls.2021.768347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/09/2021] [Indexed: 05/20/2023]
Abstract
Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root, leaf, and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- *Correspondence: Natalia Borowska-Zuchowska,
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Serhii Mykhailyk
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Wartini
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Artur Pinski
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Hasterok R, Wang K, Jenkins G. Progressive refinement of the karyotyping of Brachypodium genomes. THE NEW PHYTOLOGIST 2020; 227:1668-1675. [PMID: 31774178 DOI: 10.1111/nph.16342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/05/2019] [Indexed: 05/23/2023]
Abstract
Brachypodium distachyon is a weedy grass species that is firmly established as a model for the comparative and functional genomics of temperate cereals and grasses. Its simple, nuclear genome of five chromosomes contrasts it with other relatives of the genus with different, and usually higher, basic chromosome numbers and ploidy levels. This variation in karyotypic structure affords the possibility of reconstructing evolutionary pathways that have shaped the genome structure of extant species. This Tansley insight documents how key refinements in molecular cytogenetic approaches, from simple fluorescence in situ hybridization to comparative chromosome barcoding, have enabled genome structure studies and yielded valuable information about the drivers of karyotypic reorganization and evolution in the model grass genus Brachypodium.
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Affiliation(s)
- Robert Hasterok
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou Fujian, 350002, China
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Edward Llwyd Building, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK
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Borowska‐Zuchowska N, Kovarik A, Robaszkiewicz E, Tuna M, Tuna GS, Gordon S, Vogel JP, Hasterok R. The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1810-1825. [PMID: 32506573 PMCID: PMC7497271 DOI: 10.1111/tpj.14869] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 05/22/2023]
Abstract
Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.
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Affiliation(s)
- Natalia Borowska‐Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Ales Kovarik
- Department of Molecular EpigeneticsInstitute of BiophysicsAcademy of Sciences of the Czech Republic, v.v.i.Královopolská 135Brno612 65Czech Republic
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Metin Tuna
- Department of Field CropsFaculty of AgricultureTekirdag Namik Kemal UniversitySuleymanpasaTekirdag59030Turkey
| | | | - Sean Gordon
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
| | - John P. Vogel
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
- University CaliforniaBerkeley, BerkeleyCA94720USA
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
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Glombik M, Bačovský V, Hobza R, Kopecký D. Competition of Parental Genomes in Plant Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:200. [PMID: 32158461 PMCID: PMC7052263 DOI: 10.3389/fpls.2020.00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/11/2020] [Indexed: 05/17/2023]
Abstract
Interspecific hybridization represents one of the main mechanisms of plant speciation. Merging of two genomes from different subspecies, species, or even genera is frequently accompanied by whole-genome duplication (WGD). Besides its evolutionary role, interspecific hybridization has also been successfully implemented in multiple breeding programs. Interspecific hybrids combine agronomic traits of two crop species or can be used to introgress specific loci of interests, such as those for resistance against abiotic or biotic stresses. The genomes of newly established interspecific hybrids (both allopolyploids and homoploids) undergo dramatic changes, including chromosome rearrangements, amplifications of tandem repeats, activation of mobile repetitive elements, and gene expression modifications. To ensure genome stability and proper transmission of chromosomes from both parental genomes into subsequent generations, allopolyploids often evolve mechanisms regulating chromosome pairing. Such regulatory systems allow only pairing of homologous chromosomes and hamper pairing of homoeologs. Despite such regulatory systems, several hybrid examples with frequent homoeologous chromosome pairing have been reported. These reports open a way for the replacement of one parental genome by the other. In this review, we provide an overview of the current knowledge of genomic changes in interspecific homoploid and allopolyploid hybrids, with strictly homologous pairing and with relaxed pairing of homoeologs.
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Affiliation(s)
- Marek Glombik
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Roman Hobza
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
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Borowska-Zuchowska N, Robaszkiewicz E, Wolny E, Betekhtin A, Hasterok R. Ribosomal DNA loci derived from Brachypodium stacei are switched off for major parts of the life cycle of Brachypodium hybridum. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:805-815. [PMID: 30481334 PMCID: PMC6363085 DOI: 10.1093/jxb/ery425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/21/2018] [Indexed: 05/15/2023]
Abstract
Nucleolar dominance is an epigenetic phenomenon that occurs in some plant and animal allopolyploids and hybrids, whereby only one ancestral set of 35S rRNA genes retains the ability to form the nucleolus while the rDNA loci derived from the other progenitor are transcriptionally silenced. There is substantial evidence that nucleolar dominance is regulated developmentally. This study focuses upon the establishment and/or maintenance of nucleolar dominance during different stages of development in the model grass allotetraploid Brachypodium hybridum. Fluorescence in situ hybridization with a 25S rDNA probe to cells in three-dimensional cytogenetic preparations showed that nucleolar dominance is present not only in root meristematic and differentiated cells of this species, but also in male meiocytes at prophase I, tetrads of microspores, and different embryonic tissues. The inactive state of Brachypodium stacei-originated rDNA loci was confirmed by silver staining. Only B. distachyon-derived 35S rDNA loci formed nucleoli in the aforementioned tissues, whereas B. stacei-like loci remained highly condensed and thus transcriptionally suppressed. The establishment of nucleolar dominance during earlier stages of B. hybridum embryo development cannot be ruled out. However, we propose that gradual pseudogenization of B. stacei-like loci in the evolution of the allotetraploid seems to be more likely.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- Correspondence:
| | - Ewa Robaszkiewicz
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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Lusinska J, Majka J, Betekhtin A, Susek K, Wolny E, Hasterok R. Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum. ANNALS OF BOTANY 2018; 122:445-459. [PMID: 29893795 PMCID: PMC6110338 DOI: 10.1093/aob/mcy086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/12/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490-496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs). METHODS Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones. KEY RESULTS All species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2, Os8, Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement. CONCLUSIONS mcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid.
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Affiliation(s)
- Joanna Lusinska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Majka
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Karolina Susek
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- For correspondence. E-mail
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Martínez LM, Fernández-Ocaña A, Rey PJ, Salido T, Amil-Ruiz F, Manzaneda AJ. Variation in functional responses to water stress and differentiation between natural allopolyploid populations in the Brachypodium distachyon species complex. ANNALS OF BOTANY 2018; 121:1369-1382. [PMID: 29893879 PMCID: PMC6007385 DOI: 10.1093/aob/mcy037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/26/2018] [Indexed: 05/21/2023]
Abstract
Background and Aims Some polyploid species show enhanced physiological tolerance to drought compared with their progenitors. However, very few studies have examined the consistency of physiological drought response between genetically differentiated natural polyploid populations, which is key to evaluation of the importance of adaptive evolution after polyploidization in those systems where drought exerts a selective pressure. Methods A comparative functional approach was used to investigate differentiation of drought-tolerance-related traits in the Brachypodium species complex, a model system for grass polyploid adaptive speciation and functional genomics that comprises three closely related annual species: the two diploid parents, B. distachyon and B. stacei, and the allotetraploid derived from them, B. hybridum. Differentiation of drought-tolerance-related traits between ten genetically distinct B. hybridum populations and its ecological correlates was further analysed. Key Results The functional drought response is overall well differentiated between Brachypodium species. Brachypodium hybridum allotetraploids showed a transgressive expression pattern in leaf phytohormone content in response to drought. In contrast, other B. hybridum physiological traits correlated to B. stacei ones. Particularly, proline and water content were the traits that best discriminated these species from B. distachyon under drought. Conclusions After polyploid formation and/or colonization, B. hybridum populations have adaptively diverged physiologically and genetically in response to variations in aridity.
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Affiliation(s)
- Luisa M Martínez
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Ana Fernández-Ocaña
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Pedro J Rey
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Teresa Salido
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Francisco Amil-Ruiz
- Bioinformatics Unit, Central Service for Research Support (SCAI), University of Córdoba, Córdoba, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
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Re-exploration of U's Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences. Sci Rep 2018; 8:7353. [PMID: 29743507 PMCID: PMC5943242 DOI: 10.1038/s41598-018-25585-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/24/2018] [Indexed: 12/31/2022] Open
Abstract
The concept of U's triangle, which revealed the importance of polyploidization in plant genome evolution, described natural allopolyploidization events in Brassica using three diploids [B. rapa (A genome), B. nigra (B), and B. oleracea (C)] and derived allotetraploids [B. juncea (AB genome), B. napus (AC), and B. carinata (BC)]. However, comprehensive understanding of Brassica genome evolution has not been fully achieved. Here, we performed low-coverage (2-6×) whole-genome sequencing of 28 accessions of Brassica as well as of Raphanus sativus [R genome] to explore the evolution of six Brassica species based on chloroplast genome and ribosomal DNA variations. Our phylogenomic analyses led to two main conclusions. (1) Intra-species-level chloroplast genome variations are low in the three allotetraploids (2~7 SNPs), but rich and variable in each diploid species (7~193 SNPs). (2) Three allotetraploids maintain two 45SnrDNA types derived from both ancestral species with maternal dominance. Furthermore, this study sheds light on the maternal origin of the AC chloroplast genome. Overall, this study clarifies the genetic relationships of U's triangle species based on a comprehensive genomics approach and provides important genomic resources for correlative and evolutionary studies.
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Mirzaghaderi G, Abdolmalaki Z, Zohouri M, Moradi Z, Mason AS. Dynamic nucleolar activity in wheat × Aegilops hybrids: evidence of C-genome dominance. PLANT CELL REPORTS 2017; 36:1277-1285. [PMID: 28456843 DOI: 10.1007/s00299-017-2152-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
NOR loci of C-subgenome are dominant in wheat × Aegilops interspecific hybrids, which may have evolutionary implications for wheat group genome dynamics and evolution. After interspecific hybridisation, some genes are often expressed from only one of the progenitor species, shaping subsequent allopolyploid genome evolution processes. A well-known example is nucleolar dominance, i.e. the formation of cell nucleoli from chromosomes of only one parental species. We studied nucleolar organizing regions (NORs) in diploid Aegilops markgrafii (syn: Ae. caudata; CC), Ae. umbellulata (UU), allotetraploids Aegilops cylindrica (CcCcDcDc) and Ae. triuncialis (CtCtUtUt), synthetic interspecific F1 hybrids between these two allotetraploids and bread wheat (Triticum aestivum, AABBDD) and in F3 generation hybrids with genome composition AABBDDCtCtUtUt using silver staining and fluorescence in situ hybridization (FISH). In Ae. markgrafii (CC), NORs of both 1C and 5C or only 5C chromosome pairs were active in different individual cells, while only NORs on 1U chromosomes were active in Ae. umbellulata (UU). Although all 35S rDNA loci of the Ct subgenome (located on 1Ct and 5Ct) were active in Ae. triuncialis, only one pair (occupying either 1Cc or 5Cc) was active in Ae. cylindrica, depending on the genotype studied. These C-genome expression patterns were transmitted to the F1 and F3 generations. Wheat chromosome NOR activity was variable in Ae. triuncialis × T. aestivum F1 seeds, but silenced by the F3 generation. No effect of maternal or paternal cross direction was observed. These results indicate that C-subgenome NOR loci are dominant in wheat × Aegilops interspecific hybrids, which may have evolutionary implications for wheat group genome dynamics and allopolyploid evolution.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran.
| | - Zinat Abdolmalaki
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Mohsen Zohouri
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Zeinab Moradi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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Borowska-Zuchowska N, Hasterok R. Epigenetics of the preferential silencing of Brachypodium stacei-originated 35S rDNA loci in the allotetraploid grass Brachypodium hybridum. Sci Rep 2017; 7:5260. [PMID: 28706212 PMCID: PMC5509716 DOI: 10.1038/s41598-017-05413-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/30/2017] [Indexed: 01/16/2023] Open
Abstract
Nucleolar dominance (ND), initially described as ‘differential amphiplasty’, is a phenomenon observed in some plant and animal allopolyploids and hybrids in which the selective suppression of the activity of 35S rRNA gene loci that have been inherited from one of the two or more ancestral genomes occurs. Although more than 80 years have passed since the discovery of ND, there is still a significant lack in our understanding of the mechanisms that determine this phenomenon. Here, we aimed to investigate the epigenetic status of 35S rRNA gene loci in the monocotyledonous Brachypodium hybridum, which is an allotetraploid that has resulted from a cross between B. distachyon and B. stacei. We revealed that the repressed B. stacei-inherited rDNA loci are characterised by a high level of DNA methylation. The global hypomethylation of B. hybridum nuclear DNA induced by 5-azacytidine, however, seems to be insufficient for the transcriptional reactivation of these loci, which indicates that factors other than DNA methylation are behind the suppression of B. stacei-originated loci. We also showed that the transcriptionally active and silenced fractions of rRNA genes that had been inherited from B. distachyon occupy different domains within the chromocentres adjacent to the nucleolus, depending on their epigenetic status.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032, Katowice, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032, Katowice, Poland
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Dinh Thi VH, Coriton O, Le Clainche I, Arnaud D, Gordon SP, Linc G, Catalan P, Hasterok R, Vogel JP, Jahier J, Chalhoub B. Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei. PLoS One 2016; 11:e0167171. [PMID: 27936041 PMCID: PMC5147888 DOI: 10.1371/journal.pone.0167171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/09/2016] [Indexed: 11/19/2022] Open
Abstract
Brachypodium hybridum (2n = 30) is a natural allopolyploid with highly divergent sub-genomes derived from two extant diploid species, B. distachyon (2n = 10) and B. stacei (2n = 20) that differ in chromosome evolution and number. We created synthetic B. hybridum allotetraploids by hybridizing various lines of B. distachyon and B. stacei. The initial amphihaploid F1 interspecific hybrids were obtained at low frequencies when B. distachyon was used as the maternal parent (0.15% or 0.245% depending on the line used) and were sterile. No hybrids were obtained from reciprocal crosses or when autotetraploids of the parental species were crossed. Colchicine treatment was used to double the genome of the F1 amphihaploid lines leading to allotetraploids. The genome-doubled F1 plants produced a few S1 (first selfed generation) seeds after self-pollination. S1 plants from one parental combination (Bd3-1×Bsta5) were fertile and gave rise to further generations whereas those of another parental combination (Bd21×ABR114) were sterile, illustrating the importance of the parental lineages crossed. The synthetic allotetraploids were stable and resembled the natural B. hybridum at the phenotypic, cytogenetic and genomic levels. The successful creation of synthetic B. hybridum offers the possibility to study changes in genome structure and regulation at the earliest stages of allopolyploid formation in comparison with the parental species and natural B. hybridum.
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Affiliation(s)
- Vinh Ha Dinh Thi
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
| | - Olivier Coriton
- Unité Mixte de Recherches INRA, Agrocampus Rennes—Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes, Le Rheu, France
| | - Isabelle Le Clainche
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
| | - Dominique Arnaud
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
| | - Sean P. Gordon
- DOE Joint Genome Institute, Walnut Creek, United States of America
| | - Gabriella Linc
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences,Martonvásár, Brunszvik u 2, Hungary
| | - Pilar Catalan
- Department of Agriculture and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Tomsk, Russia
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia,Katowice, Poland
| | - John P. Vogel
- DOE Joint Genome Institute, Walnut Creek, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, United States of America
| | - Joseph Jahier
- Unité Mixte de Recherches INRA, Agrocampus Rennes—Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes, Le Rheu, France
| | - Boulos Chalhoub
- Organization and evolution of complex genomes, Institut National de la Recherche agronomique, Université d’Evry Val d’Essonne, Evry, France
- Institute of System and Synthetic Biology, Genopole, Centre National de la Recherche Scientifique, Université d’Evry Val d’Essonne, Université Paris-Saclay, Evry, France
- * E-mail:
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Borowska-Zuchowska N, Kwasniewski M, Hasterok R. Cytomolecular Analysis of Ribosomal DNA Evolution in a Natural Allotetraploid Brachypodium hybridum and Its Putative Ancestors-Dissecting Complex Repetitive Structure of Intergenic Spacers. FRONTIERS IN PLANT SCIENCE 2016; 7:1499. [PMID: 27790225 PMCID: PMC5064635 DOI: 10.3389/fpls.2016.01499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/20/2016] [Indexed: 05/22/2023]
Abstract
Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n = 30), which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n = 10) and B. stacei (2n = 20). Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs) from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.
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Affiliation(s)
- Natalia Borowska-Zuchowska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
- *Correspondence: Natalia Borowska-Zuchowska
| | - Miroslaw Kwasniewski
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
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The Genus Brachypodium as a Model for Perenniality and Polyploidy. GENETICS AND GENOMICS OF BRACHYPODIUM 2015. [DOI: 10.1007/7397_2015_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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López-Alvarez D, López-Herranz ML, Betekhtin A, Catalán P. A DNA barcoding method to discriminate between the model plant Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). PLoS One 2012; 7:e51058. [PMID: 23240000 PMCID: PMC3519806 DOI: 10.1371/journal.pone.0051058] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/29/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). METHODOLOGY/PRINCIPAL FINDINGS We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. CONCLUSION/SIGNIFICANCE Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.
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Affiliation(s)
- Diana López-Alvarez
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
| | | | - Alexander Betekhtin
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
| | - Pilar Catalán
- Department of Agriculture and Environmental Sciences, University of Zaragoza, Huesca, Spain
- * E-mail:
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Intraspecific polymorphism of ribosomal DNA loci number and morphology in Brachypodium pinnatum and Brachypodium sylvaticum. Cell Mol Biol Lett 2012; 17:526-41. [PMID: 22893263 PMCID: PMC6275692 DOI: 10.2478/s11658-012-0025-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 08/09/2012] [Indexed: 11/20/2022] Open
Abstract
The genus Brachypodium has become the target of extensive cytomolecular studies since one of its representatives, B. distachyon, has been accepted as a model plant for temperate cereals and forage grasses. Recent preliminary studies suggested that intraspecific rDNA polymorphism can occur in at least two members of the genus, B. sylvaticum and B. pinnatum, so the aim of this study was to further analyse this phenomenon. FISH with 25S rDNA and 5S rDNA probes was performed on somatic metaphase chromosomes, supplemented by the silver staining technique which distinguishes transcriptionally active from inactive 18S-5.8S-25S rDNA loci. The number, size and chromosomal distribution of 5S rDNA loci were very constant: two loci were invariably observed in all studied diploid accessions of both species, while four 5S rDNA loci were present in the tetraploid B. pinnatum. In contrast to 5S rDNA loci, those of the 35S rDNA were more variable. Two or three loci were observed in the diploid B. pinnatum and four in tetraploid accessions. In chromosome complements of B. sylvaticum accessions from two to six 35S rDNA sites were detected. Regardless of total rDNA locus number, only two were transcriptionally active in diploid accessions of both species, while two or four were active in the tetraploid B. pinnatum. Additionally, the fluorescent CMA/DAPI banding method was used to identify the relation between rDNA sites and CMA+ bands. It was revealed that the number and chromosomal distribution of CMA+ bands are in congruence only with 35S rDNA loci which gave strong FISH signals.
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21
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Lee SH, Choi HW, Sung JS, Bang JW. Inter-genomic relationships among three medicinal herbs: Cnidium officinale, Ligusticum chuanxiong and Angelica polymorpha. Genes Genomics 2010. [DOI: 10.1007/s13258-009-0871-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Huo N, Vogel JP, Lazo GR, You FM, Ma Y, McMahon S, Dvorak J, Anderson OD, Luo MC, Gu YQ. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. PLANT MOLECULAR BIOLOGY 2009; 70:47-61. [PMID: 19184460 DOI: 10.1007/s11103-009-9456-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 01/07/2009] [Indexed: 05/22/2023]
Abstract
Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that approximately 26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and approximately 1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that approximately 17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (approximately 9 kb/gene) and lower repeat DNA content (approximately 13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.
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Affiliation(s)
- Naxin Huo
- Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
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